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Andres S. Espindola

Assistant Professor

IBMF

Oklahoma State University

Assistant professor at the Department of Entomology and Plant Pathology and the Institute for Biosecurity and Microbial Forensics (IBMF) at Oklahoma State University. My background includes computational and molecular biology. My work focuses on developing bioinformatic and molecular tools to detect plant pathogen in high throughput data. I’m the the lead developer of Microbe Finder (MiFi), a graphical user interface that is used to create and validate e-probes for the detection of pathogens in high-throughput sequencing (HTS) data. MiFi has been used to evaluate e-probes for Citrus, Poaceae, Roses, Blueberries, Pomes and a variety of regulated pathogens on multiple hosts. Additionally, my research has been instrumental to develop protocols that increase pathogen availability in HTS libraries, ultimately increasing HTS sensitivity in detection using Target Specific Reverse Primer Pools (TASPERT). I’m also actively working on computational modeling to predict crop productivity and pathogen detection. I have extensive experience analyzing, genomic, transcriptomic and metagenomic big data from long and short read HTS platforms. By using HTS we aim to develop the appropriate protocols to detect any pathogen in any plant sample. Currently I am using Oxford Nanopore Technologies (ONT) minION sequencer to validate portability of sequencing devices for diagnostics.

Interests

  • Bioinformatics
  • Plant Pathology
  • Molecular Diagnostics
  • Metagenomics
  • Microbiome

Education

  • PhD in Plant Pathology, 2016

    Oklahoma State University

  • Bioinformatics Certificate, 2016

    Oklahoma State University

  • MS in Entomology and Plant Pathology, 2013

    Oklahoma State University

  • Biotechnology Engineering, 2009

    Army Polytechnic School ESPE - Ecuador

Expertise

Molecular Biology

PCR, real-time PCR, cloning

Plant Microbiome

plant rhizosphere

Python

biopython, strings, arrays

R statistics

differential gene expression, RNAseq

High-throughput Sequencing

MinION, Illumina, metagenomics, metatranscriptomics

Experience

 
 
 
 
 

Assistant Professor

Institute for Biosecurity and Microbial Forensics

Sep 2022 – Present Stilwater, OK
Responsibilities include:
 
 
 
 
 

Assistant Research Professor

NIMFFAB

Nov 2018 – Aug 2022 Stilwater, OK
Responsibilities include:

  • Develop Microbe Finder (MiFi) MinION for Plant Pathogens, Animal pathogens and forensics.
  • Graphical User Interface of MiFi (http://bioinfo.okstate.edu)
  • Grapevine virus detection with MinION and MiFi
  • Rose virus detection in a single shot with MinION and MiFi
  • Citrus virus and bacteria detection with MinION and MiFi.
  • E-probe design and validation for the detection of Ralstonia species in blueberry
 
 
 
 
 

Postdoctoral Fellow

NIMFFAB

Jan 2017 – Nov 2018 Stilwater, OK
Responsibilities include:

  • EDNA MinION for Plant Pathogens
  • Oxford Nanopore Sequencing (MinION) validation for plant pathogen detection in Grapes, Roses, Cucurbits.
  • Use RNA sequencing and eprobes to determine Aspergillus flavus presence in soil.
  • MinION sequencing for Grapevine pathogen detection.
 
 
 
 
 

Research Assistant and Teaching Assistant

Oklahoma State University

Jan 2011 – Dec 2016 Oklahoma
Developed bioinformatic tools for plant pathogen detection using high-throughput sequencing Responsibilities include: * Analyze the genome and transcriptome of Sclerotinia minor and Aspergillus flavus by using next-generation sequencing. * Conduct a profound statistical analysis in R for molecular biology projects including PCR, qPCR and sequencing

Extramural Funding

Metagenomic probes for the rapid identification of the microbiome community in a wheat rhizosphere model system

Award: $220,000

E-probe Diagnostic Nucleic acid Analysis (EDNA) for quarantine detection and discrimination of Poaceae viruses

$114,449

Detection of detrimental viruses and viroids in high value chrysanthemums in Oklahoma

$87,506

Electronic Diagnostic Nucleic Acid Analysis (EDNA) for accurate detection and discrimination of Rose Viruses

$50,000

Detection of Grapevine viruses using high-throughput sequencing

Two years total: $99,871

Recent Posts

Git Basics and Advanced

This is a basic post on how to interact with github through command line

Installing and configuring BLAST in Linux

Whenever I’m setting up new virtual machines to work on them, it is usually a problem when I try to run blast and I have to point …

Removing host sequences in microbiome datasets

Analyzing metagenomic or metatranscriptomic sequencing datasets can cause a lot of trouble when excesive depth is utilized. This is …

Using git with ssh keys

This is a post for github advances users that don’t want to type their username and password everytime a change is commited and …

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